Atomistry » Magnesium » PDB 3srf-3t2b » 3srf
Atomistry »
  Magnesium »
    PDB 3srf-3t2b »
      3srf »

Magnesium in PDB 3srf: Human M1 Pyruvate Kinase

Enzymatic activity of Human M1 Pyruvate Kinase

All present enzymatic activity of Human M1 Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Human M1 Pyruvate Kinase, PDB code: 3srf was solved by H.P.Morgan, F.O'reilly, R.Palmer, I.W.Mcnae, M.W.Nowicki, M.A.Wear, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 238.003, 192.222, 109.060, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 28

Other elements in 3srf:

The structure of Human M1 Pyruvate Kinase also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human M1 Pyruvate Kinase (pdb code 3srf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human M1 Pyruvate Kinase, PDB code: 3srf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 1 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg533

b:45.9
occ:1.00
 OE1 C:GLU271 2.1 30.1 1.0
OD2 C:ASP295 2.7 32.5 1.0
O2 C:PYR534 2.8 46.1 1.0
CD C:GLU271 3.1 30.0 1.0
C1 C:PYR534 3.3 46.4 1.0
CG C:ASP295 3.4 32.2 1.0
OE2 C:GLU271 3.6 29.9 1.0
NZ C:LYS269 3.8 25.4 1.0
O1 C:PYR534 3.9 46.5 1.0
C2 C:PYR534 4.0 46.4 1.0
O3 C:PYR534 4.0 46.2 1.0
CB C:ASP295 4.1 31.7 1.0
CZ C:PHE243 4.1 33.7 1.0
CE C:LYS269 4.2 26.7 1.0
OD1 C:ASP295 4.2 32.7 1.0
CE1 C:PHE243 4.3 34.0 1.0
CG C:GLU271 4.4 29.7 1.0
CE2 C:PHE243 4.8 33.5 1.0
N C:ASP295 4.9 31.4 1.0

Magnesium binding site 2 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 2 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg533

b:27.0
occ:1.00
 OD2 A:ASP295 2.1 32.9 1.0
O3 A:PYR534 2.4 39.6 1.0
O2 A:PYR534 2.4 38.3 1.0
OE1 A:GLU271 2.6 30.4 1.0
C2 A:PYR534 3.1 39.1 1.0
C1 A:PYR534 3.2 38.6 1.0
CG A:ASP295 3.3 32.1 1.0
O A:HOH594 3.5 13.5 1.0
CD A:GLU271 3.7 29.9 1.0
NZ A:LYS269 3.9 24.8 1.0
OE2 A:GLU271 4.1 29.6 1.0
CB A:ASP295 4.2 31.6 1.0
OD1 A:ASP295 4.2 32.5 1.0
O A:HOH551 4.2 25.9 1.0
O1 A:PYR534 4.4 38.1 1.0
C3 A:PYR534 4.6 38.8 1.0
O A:HOH587 4.6 37.3 1.0
CE A:LYS269 4.6 24.4 1.0
CE1 A:PHE243 4.7 34.0 1.0
N A:ASP295 4.8 31.6 1.0
CZ A:PHE243 4.8 33.9 1.0
CG A:GLU271 5.0 28.6 1.0

Magnesium binding site 3 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 3 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg533

b:26.3
occ:1.00
 O2 B:PYR534 2.0 42.7 1.0
OD2 B:ASP295 2.1 32.6 1.0
OE1 B:GLU271 2.1 34.8 1.0
C1 B:PYR534 2.9 43.0 1.0
O3 B:PYR534 2.9 43.1 1.0
CG B:ASP295 3.2 32.0 1.0
CD B:GLU271 3.3 34.4 1.0
C2 B:PYR534 3.3 43.1 1.0
CB B:ASP295 3.8 31.4 1.0
OE2 B:GLU271 3.8 34.5 1.0
O1 B:PYR534 4.0 43.4 1.0
NZ B:LYS269 4.2 27.3 1.0
OD1 B:ASP295 4.3 32.6 1.0
CE B:LYS269 4.4 28.3 1.0
CB B:ALA292 4.5 27.5 1.0
CG B:GLU271 4.5 33.6 1.0
N B:ASP295 4.6 30.7 1.0
CE1 B:PHE243 4.6 34.4 1.0
K B:K532 4.8 94.2 1.0
C3 B:PYR534 4.8 43.0 1.0
CA B:ASP295 4.8 31.3 1.0
CZ B:PHE243 4.9 34.2 1.0

Magnesium binding site 4 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 4 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg533

b:51.2
occ:1.00
 OD2 D:ASP295 2.1 34.5 1.0
OE1 D:GLU271 2.2 34.2 1.0
O3 D:PYR534 2.4 51.6 1.0
O2 D:PYR534 2.6 51.8 1.0
O D:HOH556 3.0 10.2 1.0
C2 D:PYR534 3.2 52.1 1.0
CG D:ASP295 3.3 34.4 1.0
C1 D:PYR534 3.3 51.9 1.0
CD D:GLU271 3.4 34.3 1.0
CZ D:PHE243 3.9 36.6 1.0
NZ D:LYS269 4.0 29.4 1.0
OE2 D:GLU271 4.0 34.4 1.0
CE1 D:PHE243 4.0 36.6 1.0
CB D:ASP295 4.0 34.1 1.0
OD1 D:ASP295 4.2 34.6 1.0
CG D:GLU271 4.4 33.8 1.0
O1 D:PYR534 4.5 52.0 1.0
K D:K532 4.7 48.5 1.0
C3 D:PYR534 4.7 52.4 1.0
CE D:LYS269 4.7 29.7 1.0
CE2 D:PHE243 4.8 36.6 1.0
OG D:SER242 4.9 34.1 1.0
CD1 D:PHE243 5.0 36.1 1.0

Magnesium binding site 5 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 5 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg533

b:58.5
occ:1.00
 OD2 E:ASP295 2.0 49.3 1.0
OE1 E:GLU271 2.0 54.6 1.0
O2 E:PYR534 2.3 62.9 1.0
O3 E:PYR534 2.9 63.2 1.0
CD E:GLU271 3.1 54.6 1.0
CG E:ASP295 3.2 49.5 1.0
C1 E:PYR534 3.2 63.2 1.0
C2 E:PYR534 3.4 63.3 1.0
NZ E:LYS269 3.5 52.2 1.0
OE2 E:GLU271 3.7 54.7 1.0
CB E:ASP295 3.8 49.2 1.0
CE1 E:PHE243 3.9 59.2 1.0
CZ E:PHE243 4.1 59.2 1.0
OD1 E:ASP295 4.1 50.0 1.0
CE E:LYS269 4.2 52.3 1.0
K E:K532 4.3 85.0 1.0
CG E:GLU271 4.3 54.3 1.0
O1 E:PYR534 4.3 63.1 1.0
CD1 E:PHE243 4.8 59.0 1.0
C3 E:PYR534 4.9 63.1 1.0

Magnesium binding site 6 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 6 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg533

b:21.2
occ:1.00
 OE1 F:GLU271 1.9 30.6 1.0
O2 F:PYR534 2.1 38.8 1.0
OD2 F:ASP295 2.1 37.5 1.0
O3 F:PYR534 2.7 39.0 1.0
C1 F:PYR534 3.0 38.9 1.0
CD F:GLU271 3.0 30.4 1.0
CG F:ASP295 3.2 36.7 1.0
C2 F:PYR534 3.2 39.0 1.0
OE2 F:GLU271 3.4 30.8 1.0
CB F:ASP295 3.6 35.8 1.0
CZ F:PHE243 4.1 33.4 1.0
O1 F:PYR534 4.1 38.8 1.0
NZ F:LYS269 4.1 27.2 1.0
CE F:LYS269 4.2 27.3 1.0
OD1 F:ASP295 4.3 37.8 1.0
CG F:GLU271 4.3 29.9 1.0
CE1 F:PHE243 4.5 33.4 1.0
CB F:ALA292 4.5 33.7 1.0
CE2 F:PHE243 4.5 33.5 1.0
O F:HOH581 4.6 13.4 1.0
N F:ASP295 4.7 35.4 1.0
C3 F:PYR534 4.7 38.8 1.0
CB F:GLU271 4.8 29.4 1.0
CA F:ASP295 4.8 35.6 1.0

Magnesium binding site 7 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 7 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg533

b:33.5
occ:1.00
 OD2 G:ASP295 2.0 36.1 1.0
OE1 G:GLU271 2.0 40.9 1.0
O2 G:PYR534 2.1 67.5 1.0
O G:HOH584 2.5 31.0 1.0
O3 G:PYR534 2.7 66.8 1.0
C1 G:PYR534 3.0 67.2 1.0
CG G:ASP295 3.1 36.2 1.0
CD G:GLU271 3.2 41.3 1.0
C2 G:PYR534 3.3 67.1 1.0
OE2 G:GLU271 3.6 41.5 1.0
CB G:ASP295 3.7 35.9 1.0
NZ G:LYS269 3.9 39.4 1.0
OD1 G:ASP295 4.2 36.6 1.0
O G:HOH585 4.2 6.1 1.0
O1 G:PYR534 4.2 67.1 1.0
CE G:LYS269 4.4 39.6 1.0
CG G:GLU271 4.4 41.3 1.0
CZ G:PHE243 4.5 47.0 1.0
CE1 G:PHE243 4.6 46.9 1.0
N G:ASP295 4.6 35.9 1.0
CA G:ASP295 4.8 35.8 1.0
C3 G:PYR534 4.8 66.9 1.0
CB G:GLU271 4.9 41.4 1.0
K G:K532 4.9 60.7 1.0
CB G:ALA292 4.9 36.8 1.0

Magnesium binding site 8 out of 8 in 3srf

Go back to Magnesium Binding Sites List in 3srf
Magnesium binding site 8 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg533

b:14.2
occ:1.00
 OE1 H:GLU271 2.1 31.0 1.0
OD2 H:ASP295 2.2 34.9 1.0
O2 H:PYR534 2.7 69.8 1.0
C1 H:PYR534 3.1 70.3 1.0
CD H:GLU271 3.2 31.7 1.0
O3 H:PYR534 3.2 70.0 1.0
C2 H:PYR534 3.4 70.1 1.0
CG H:ASP295 3.4 34.8 1.0
NZ H:LYS269 3.5 25.8 1.0
CE H:LYS269 3.6 27.1 1.0
OE2 H:GLU271 3.8 32.3 1.0
O1 H:PYR534 3.9 70.8 1.0
CB H:ASP295 4.2 34.4 1.0
CG H:GLU271 4.3 31.3 1.0
CB H:ALA292 4.3 31.1 1.0
OD1 H:ASP295 4.4 35.5 1.0
C3 H:PYR534 4.6 69.7 1.0
CZ H:PHE243 4.9 35.5 1.0
CB H:GLU271 5.0 31.0 1.0

Reference:

H.P.Morgan, F.O'reilly, R.Palmer, I.W.Mcnae, M.W.Nowicki, M.A.Wear, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Allosetric Regulation of M2 Pyruvate Kinase. To Be Published.
Page generated: Mon Dec 14 08:51:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy